Artificial Genetic Sets Composed of Size‐Expanded Base Pairs
Abstract
We describe in this Minireview the synthesis, properties, and applications of artificial genetic sets built from base pairs that are larger than the natural Watson–Crick architecture. Such designed systems are being explored by several research groups to investigate basic chemical questions regarding the functions of the genetic information storage systems and thus of the origin and evolution of life. For example, is the terrestrial DNA structure the only viable one, or can other architectures function as well? Working outside the constraints of purine–pyrimidine geometry provides more chemical flexibility in design, and the added size confers useful properties such as high binding affinity and helix stability as well as fluorescence. These features are useful for the investigation of fundamental biochemical questions as well as in the development of new biotechnological, biomedical, and nanostructural tools and methods.
Number of times cited: 31
- Aditya R. Pote, Raghu Vannam, Alissa Richard, José Gascón and Mark W. Peczuh, Formation of and Glycosylation with Per‐O‐Acetyl Septanosyl Halides: Rationalizing Complex Reactivity En Route to p‐Nitrophenyl Septanosides, European Journal of Organic Chemistry, 2018, 14, (1709-1719), (2018).
- Brooke A. Anderson and Ramanarayanan Krishnamurthy, Heterogeneous Pyrophosphate‐Linked DNA–Oligonucleotides: Aversion to DNA but Affinity for RNA, Chemistry – A European Journal, 24, 26, (6837-6842), (2018).
- Rohini Keshava, Rohan Mitra, Mohan L. Gope and Rajalakshmi Gope, Synthetic Biology, Omics Technologies and Bio-Engineering, 10.1016/B978-0-12-804659-3.00004-X, (63-93), (2018).
- Amit M. Jabgunde, Faten Jaziri, Omprakash Bande, Matheus Froeyen, Mikhail Abramov, Hoai Nguyen, Guy Schepers, Eveline Lescrinier, Vitor B. Pinheiro, Valérie Pezo, Philippe Marlière and Piet Herdewijn, Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo, Chemistry – A European Journal, 24, 48, (12695-12707), (2018).
- Tim Efthymiou, Jesse Gavette, Matthias Stoop, Francesco De Riccardis, Mathy Froeyen, Piet Herdewijn and Ramanarayanan Krishnamurthy, Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems, Chemistry – A European Journal, 24, 49, (12811-12819), (2018).
- A. S. Prakasha Gowda, Marietta Lee and Thomas E. Spratt, N2‐Substituted 2′‐Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ, Angewandte Chemie International Edition, 56, 10, (2628-2631), (2017).
- Simon Ausländer, David Ausländer and Martin Fussenegger, Synthetic Biology—The Synthesis of Biology, Angewandte Chemie International Edition, 56, 23, (6396-6419), (2017).
- A. S. Prakasha Gowda, Marietta Lee and Thomas E. Spratt, N2‐Substituted 2′‐Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ, Angewandte Chemie, 129, 10, (2672-2675), (2017).
- Subhendu Sekhar Bag and Suman Kalyan Das, Design, Synthesis and Photophysical Property of a Doubly Widened Fused‐Triazolyl‐Phenanthrene Unnatural Nucleoside, ChemistrySelect, 2, 12, (3577-3583), (2017).
- Simon Ausländer, David Ausländer and Martin Fussenegger, , Angewandte Chemie, 129, 23, (6494-6519), (2017).
- Saki Matsumoto, Kei Iida, Asako Murata, Masatsugu Denawa, Masatoshi Hagiwara and Kazuhiko Nakatani, Synthetic ligand promotes gene expression by affecting GC sequence in promoter, Bioorganic & Medicinal Chemistry Letters, 10.1016/j.bmcl.2017.06.006, 27, 15, (3391-3394), (2017).
- Louis G. Smith, Jianbo Zhao, David H. Mathews and Douglas H. Turner, Physics‐based all‐atom modeling of RNA energetics and structure, Wiley Interdisciplinary Reviews: RNA, 8, 5, (2017).
- Michiko Kimoto and Ichiro Hirao, Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs, ACS Synthetic Biology, 10.1021/acssynbio.7b00165, 6, 10, (1944-1951), (2017).
- Malte Winnacker, Recent advances in the synthesis of functional materials by engineered and recombinant living cells, Soft Matter, 10.1039/C7SM01000A, 13, 38, (6672-6677), (2017).
- Falk Wachowius, James Attwater and Philipp Holliger, Nucleic acids: function and potential for abiogenesis, Quarterly Reviews of Biophysics, 10.1017/S0033583517000038, 50, (2017).
- Indu Negi, Preetleen Kathuria, Purshotam Sharma and Stacey D. Wetmore, How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations, Physical Chemistry Chemical Physics, 10.1039/C7CP02576A, 19, 25, (16365-16374), (2017).
- Wen-Jin Wu, Wei Yang and Ming-Daw Tsai, How DNA polymerases catalyse replication and repair with contrasting fidelity, Nature Reviews Chemistry, 1, 9, (0068), (2017).
- Pramod M. Sabale and Seergazhi G. Srivatsan, Responsive Fluorescent PNA Analogue as a Tool for Detecting G‐quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome‐Inactivating Proteins, ChemBioChem, 17, 17, (1665-1673), (2016).
- Yevgen P. Yurenko, Jan Novotný, Tymofii Yu. Nikolaienko and Radek Marek, Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties, Phys. Chem. Chem. Phys., 10.1039/C5CP05478H, 18, 3, (1615-1628), (2016).
- Nicole Avakyan, Andrea A. Greschner, Faisal Aldaye, Christopher J. Serpell, Violeta Toader, Anne Petitjean and Hanadi F. Sleiman, Reprogramming the assembly of unmodified DNA with a small molecule, Nature Chemistry, 8, 4, (368), (2016).
- Hong Cai, Mian Li, Xiao‐Rong Lin, Wei Chen, Guang‐Hui Chen, Xiao‐Chun Huang and Dan Li, Spatial, Hysteretic, and Adaptive Host–Guest Chemistry in a Metal–Organic Framework with Open Watson–Crick Sites, Angewandte Chemie, 127, 36, (10600-10605), (2015).
- Hong Cai, Mian Li, Xiao‐Rong Lin, Wei Chen, Guang‐Hui Chen, Xiao‐Chun Huang and Dan Li, Spatial, Hysteretic, and Adaptive Host–Guest Chemistry in a Metal–Organic Framework with Open Watson–Crick Sites, Angewandte Chemie International Edition, 54, 36, (10454-10459), (2015).
- Junya Chiba and Masahiko Inouye, Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C‐Nucleosides with Nonnatural Bases, Current Protocols in Nucleic Acid Chemistry, 61, 1, (4.62.1-4.62.22), (2015).
- Wataru Shirato, Junya Chiba and Masahiko Inouye, A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate, Chemical Communications, 51, 32, (7043), (2015).
- Kunihiko Morihiro, Hidekazu Hoshino, Osamu Hasegawa, Yuuya Kasahara, Kohsuke Nakajima, Masayasu Kuwahara, Shin-ichi Tsunoda and Satoshi Obika, Polymerase incorporation of a 2′-deoxynucleoside-5′-triphosphate bearing a 4-hydroxy-2-mercaptobenzimidazole nucleobase analogue, Bioorganic & Medicinal Chemistry Letters, 10.1016/j.bmcl.2015.05.075, 25, 15, (2888-2891), (2015).
- Jinxing Li, Jun Matsumoto, Takahiro Otabe, Chikara Dohno and Kazuhiko Nakatani, 2-Aminophenanthroline dimer stabilized the C–C mismatched duplex DNA, Bioorganic & Medicinal Chemistry, 10.1016/j.bmc.2014.12.062, 23, 4, (753-758), (2015).
- Leonid I. Belen'kii and Yu B. Evdokimenkova, The Literature of Heterocyclic Chemistry, Part XIII, 2012–2013, , 10.1016/bs.aihch.2015.04.002, (193-363), (2015).
- Blaise Dumat, Mattias Bood, Moa S. Wranne, Christopher P. Lawson, Anders Foller Larsen, Søren Preus, Jens Streling, Henrik Gradén, Eric Wellner, Morten Grøtli and L. Marcus Wilhelmsson, Second‐Generation Fluorescent Quadracyclic Adenine Analogues: Environment‐Responsive Probes with Enhanced Brightness, Chemistry – A European Journal, 21, 10, (4039-4048), (2015).
- Itaru Okamoto, Yuya Miyatake, Michiko Kimoto and Ichiro Hirao, High Fidelity, Efficiency and Functionalization of Ds–Px Unnatural Base Pairs in PCR Amplification for a Genetic Alphabet Expansion System, ACS Synthetic Biology, 10.1021/acssynbio.5b00253, (2016).
- Laura Albrecht, Katie Wilson and Stacey Wetmore, Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4, Molecules, 10.3390/molecules21070822, 21, 7, (822), (2016).
- Nadrian C. Seeman and Hanadi F. Sleiman, DNA nanotechnology, Nature Reviews Materials, 10.1038/natrevmats.2017.68, 3, (17068), (2017).




